TT16: Ontology Services for Semantic Applications in Healthcare and Life Sciences (ISMB 2009)

Trish has recorded her talk as a screencast as she wanted to do a demo, and she can’t trust the wireless – true enough! RESTful web services have been developed at the NCBO within BioPortal. http://rest.bioontology.org/bioportal (Note this is the prefix for all services, and if you just go to this URL there isn’t anything visible). Chose RESTful services as they are lightweight and easy to use. The main BioPortal website is http://bioportal.bioontology.org. All information on the BioPortal site is retrieved using those web services. Can store ontologies in OWL, OBO and Protege frames formats.

You can search ontologies based on a number of parameters. Much help information is available via mouseover text. You can also download ontologies that are available on BioPortal. When browsing your ontologies you can see the structure, the metadata, definitions and more. There are also ontology widgets that you can put on your own site, including jump-to feature and term selection widget. This latter one is very useful because it allows your web app to use term auto-complete without having to code it yourself!

To go into the search web services a little bit more, for instance search for “protocol”. The search can be paramaterized and filtered in many ways: which ontology to use, exact or non-exact matching, etc. The search function is especially important for ontology re-use. For instance, if you’re developing a new domain ontology, then you want to make sure you don’t reinvent the wheel and this is a good way to find out what’s out there. The next bit of the video showed using these searches via programmatic means.

BioPortal also allows you to annotate, or add notes, to ontologies. There is also an annotation tag /term cloud in the interface, which is nice :) You may see duplicates in the tag cloud – designed to be this way to show that more than one ontology has that term.. There are also hierarchy services. You can view the parent terms of a particular term, and do other sorts of queries that allow you to explore the hierarchy around a term programmatically. On the web app, they have a visualization of the hierarchy that is dynamic and you can play with.

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!